fslr: Wrapper Functions for FSL ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')

Wrapper functions that interface with 'FSL' (http:// fsl.fmrib.ox.ac.uk/fsl/fslwiki/), a powerful and commonly-used 'neuroimaging' software, using system commands. The goal is to be able to interface with 'FSL' completely in R, where you pass R objects of class 'nifti', implemented by package 'oro.nifti', and the function executes an 'FSL' command and returns an R object of class 'nifti' if desired.

AuthorJohn Muschelli <muschellij2@gmail.com>
Date of publication2016-09-28 19:35:02
MaintainerJohn Muschelli <muschellij2@gmail.com>
LicenseGPL-3
Version2.0

View on CRAN

Man pages

aux_file-methods: Extract Image aux.file attribute

bitpix-methods: Extract Image bitpix attribute

cal_max-methods: Extract Image cal.max attribute

cal_min-methods: Extract Image cal.min attribute

check_file: Wrapper for getForms with filename

checkout: Determine of Q and S forms are consistent

data_type-methods: Extract Image data_type attribute

datatype-methods: Extract Image datatype attribute

descrip-methods: Extract Image descrip attribute

dim_-methods: Extract Image dim_ attribute

download_fsl: Download FSL

dtifit: DTI Fitting Procedure from FSL

eddy_correct: Eddy Current Correction

fast: FSL FAST

fast.help: FAST help

flirt: Register using FLIRT

flirt_apply: Apply Warp from FLIRT

flirt.help: FLIRT help

fnirt: Register using FNIRT

fnirt.help: FNIRT help

fnirt_with_affine: Register using FNIRT, but doing Affine Registration as well

fnirt_with_affine_apply: Applies FLIRT then FNIRT transformations

fslabs: Absolute Value Image using FSL

fslabs.help: fslabs Help

fslacos: Arc Cosine Transform Image using FSL

fslacos.help: fslacos Help

fsladd: Add Images using FSL

fsladd.help: fsladd Help

fsl_anat: FSL Anatomical Processing Script

fsl_anat.help: fsl_anat help

fsl_applywarp: Apply Warp from FNIRT

fsl_applywarp.help: FSL applywarp help

fslasin: Arc Sine Transform Image using FSL

fslasin.help: fslasin Help

fslatan: Arc Tangent Transform Image using FSL

fslatan.help: fslatan Help

fsl_atlas_dir: Get FSL's Standard Data Directory

fslbet: Use FSL's Brain Extraction Tool (BET)

fslbet.help: Help for FSL BET

fsl_biascorrect: FSL Bias Correct

fslbin: Binarize Image using FSL

fslbin.help: fslbin Help

fslbinv: Binarized Inverse Image using FSL

fslbinv.help: fslbinv Help

fslchfiletype: FSL Change file type

fslchfiletype.help: fslchfiletype help

fslcmd: FSL Command Wrapper

fslcog: Image Center of Gravity (FSL)

fslcos: Cosine Transform Image using FSL

fslcos.help: fslcos Help

fslcpgeom: FSL Copy Geometry

fslcpgeom.help: fslcpgeom help

fsl_data_dir: Get FSL's Data Directory

fsldilate: Dilate image using FSL

fsldir: Get FSL's Directory

fsldiv: Divide Images using FSL

fsldiv.help: fsldiv Help

fsledge: Edge Strength Image using FSL

fsledge.help: fsledge Help

fslentropy: Image Mean Entropy

fslerode: Erode image using FSL

fslerode.help: fslerode Help

fslexp: Exponentiate Image using FSL

fslexp.help: fslexp Help

fslfill: Fill image holes

fslfill2: Fill image holes with dilation then erosion

fslfill.help: fslfill Help

fslhd: Get NIfTI header using FSL

fslhd.help: FSLhd help

fslhd.parse: Parse FSL Header

fslhelp: Wrapper for getting fsl help

fslindex: Index Image using FSL

fslindex.help: fslindex Help

fsllog: Log Transform Image using FSL

fsllog.help: fsllog Help

fslmask: Mask image using FSL

fslmask.help: fslmask Help

fslmaths: FSL Maths

fslmaths.help: FSL Maths Help

fslmean: Image Mean

fslmerge: Merge images using FSL

fslmerge.help: FSLMerge help

fslmul: Multiply Images using FSL

fslmul.help: fslmul Help

fslnan: Replace NaNs in Image using FSL

fslnan.help: fslnan Help

fslnanm: Mask NaNs in Image using FSL

fslnanm.help: fslnanm Help

fslorient: FSL Orient

fslorienter: Wrapper for FSL Get Orientation

fslorient.help: fslorient help

fslorient_wrap: FSL Orientation Wrappers

fslrand: Add Random Uniform Noise Image using FSL

fslrand.help: fslrand Help

fslrandn: Add Random Standard Guassian Noise Image using FSL

fslrandn.help: fslrandn Help

fslrange: Get range of an image

fslrecip: Reciprocal Image using FSL

fslrecip.help: fslrecip Help

fslrem: Modulus Remainder of 2 Images using FSL

fslrem.help: fslrem Help

fslreorient2std: FSL Orient to MNI

fslreorient2std.help: fslreorient2std help

fslroi: FSL ROI

fslsd: Image Standard Deviation

fslsin: Sine Transform Image using FSL

fslsin.help: fslsin Help

fsl_slicetimer: FSL Slice Timing Correction

fslsmooth: Gaussian smooth image using FSL

fslsmooth.help: fslsmooth Help

fslsplit: Split images using FSL

fslsplit.help: FSL Split help

fslsqr: Square Image using FSL

fslsqr.help: fslsqr Help

fslsqrt: Square Root Image using FSL

fslsqrt.help: fslsqrt Help

fslstats: FSL Stats

fslstats.help: FSL Stats Help

fsl_std_dir: Get FSL's Standard Data Directory

fslsub: Subtract Images using FSL

fslsub2: Subsample image by factor of 2

fslsub2.help: fslsub2 Help

fslsub.help: fslsub Help

fslsum: FSL Sum

fslswapdim: FSL Swap Dimensions

fslswapdim.help: fslswapdim help

fsltan: Tangent Transform Image using FSL

fsltan.help: fsltan Help

fslthresh: Threshold an image

fslthresh.help: fslthresh Help

fslval: Get value from FSL header

fslval.help: fslval help

fsl_version: Find FSL Version

fslview: Open image in FSLView

fslview.help: FSLView help

fslvol: FSL Volume in mL (or cubic centimeters)

fslvolume: Image Volume

getForms: Get Q and S Forms of orientation matrix

get.fsl: Create command declaring FSLDIR

get.fsloutput: Determine FSL output type

get.imgext: Determine extension of image based on FSLOUTPUTTYPE

have.fsl: Logical check if FSL is accessible

intent_code-methods: Extract Image intent_code attribute

intent_name-methods: Extract Image intent_name attribute

intent_p1-methods: Extract Image intent_p1 attribute

intent_p2-methods: Extract Image intent_p2 attribute

intent_p3-methods: Extract Image intent_p3 attribute

magic-methods: Extract Image magic attribute

mcflirt: FSL Motion Correction

mcflirt.help: MCFLIRT help

melodic: Run MELODIC ICA

melodic.help: MELODIC help

mni_fname: Construct MNI Filename

mni_img: Read MNI Filename

orientation-methods: Extract NIfTI 3D Image Orientation

pixdim-methods: Extract Image pixdim attribute

probtrackx: Probabilistic diffusion tractography with multiple fibre...

qform_code-methods: Extract Image qform_code attribute

run_first_all: Run FIRST All

run_first_all.help: Run FIRST All Help

scl_inter-methods: Extract Image scl_inter attribute

scl_slope-methods: Extract Image scl_slope attribute

sform_code-methods: Extract Image sform_code attribute

sizeof_hdr-methods: Extract Image sizeof_hdr attribute

slice_code-methods: Extract Image slice_code attribute

slice_duration-methods: Extract Image slice_duration attribute

slice_end-methods: Extract Image slice_end attribute

slice_start-methods: Extract Image slice_start attribute

susan: FSL SUSAN noise reduction

susan.help: FSL SUSAN Help

toffset-methods: Extract Image toffset attribute

vox_offset-methods: Extract Image vox_offset attribute

xfibres: Bayesian Estimation of Diffusion Parameters Obtained using...

Files in this package

fslr
fslr/inst
fslr/inst/CITATION
fslr/inst/doc
fslr/inst/doc/dti_data.Rmd
fslr/inst/doc/dti_data.R
fslr/inst/doc/fslr.R
fslr/inst/doc/fslr.html
fslr/inst/doc/dti_data.html
fslr/inst/doc/fslr.Rmd
fslr/NAMESPACE
fslr/R
fslr/R/intent_code.R fslr/R/fslvol.R fslr/R/fslrecip.R fslr/R/scl_inter.R fslr/R/fslnanm.R fslr/R/fslexp.R fslr/R/fslvolume.R fslr/R/fslcpgeom.R fslr/R/probtrackx.R fslr/R/fslbin.help.R fslr/R/fslsin.help.R fslr/R/fsledge.R fslr/R/applywarp.R fslr/R/fslsub2.help.R fslr/R/mcflirt.R fslr/R/fsledge.help.R fslr/R/fslchfiletype.R fslr/R/fslmask.help.R fslr/R/fsl_anat.R fslr/R/fslatan.R fslr/R/fslrandn.help.R fslr/R/fslacos.R fslr/R/susan.R fslr/R/fslnan.R fslr/R/fslsqrt.R fslr/R/fnirt.R fslr/R/fslindex.R fslr/R/mni_fname.R fslr/R/fslmean.R fslr/R/fslasin.help.R fslr/R/fslsub.R fslr/R/fsldiv.R fslr/R/sizeof_hdr.R fslr/R/fsldiv.help.R fslr/R/bitpix.R fslr/R/fslrand.help.R fslr/R/aux_file.R fslr/R/fslrem.help.R fslr/R/magic.R fslr/R/datatype.R fslr/R/fslfill2.R fslr/R/fslhd.R fslr/R/fsladd.R fslr/R/fslentropy.R fslr/R/import_methods.R fslr/R/fslatan.help.R fslr/R/fslrandn.R fslr/R/fslcos.help.R fslr/R/fslrand.R fslr/R/fslsmooth.help.R fslr/R/fsltan.R fslr/R/intent_p3.R fslr/R/cal_min.R fslr/R/fslthresh.help.R fslr/R/fslsd.R fslr/R/slice_duration.R fslr/R/intent_p1.R fslr/R/dim_.R fslr/R/sform_code.R fslr/R/fslerode.help.R fslr/R/fslabs.R fslr/R/fsl_data_dir.R fslr/R/fslsub.help.R fslr/R/slice_end.R fslr/R/fslmul.help.R fslr/R/fsllog.R fslr/R/xfibres.R fslr/R/fslrem.R fslr/R/slice_start.R fslr/R/intent_name.R fslr/R/eddy_correct.R fslr/R/fslsum.R fslr/R/data_type.R fslr/R/fsltan.help.R fslr/R/fslsplit.R fslr/R/fslsqrt.help.R fslr/R/fsl_slicetimer.R fslr/R/fslbinv.help.R fslr/R/fslsqr.R fslr/R/fslacos.help.R fslr/R/fslsqr.help.R fslr/R/fslgetorient.R fslr/R/scl_slope.R fslr/R/vox_offset.R fslr/R/fslsin.R fslr/R/fslmul.R fslr/R/qform.R fslr/R/slice_code.R fslr/R/run_first_all.R fslr/R/fsl_version.R fslr/R/fslcos.R fslr/R/sform.R fslr/R/fslindex.help.R fslr/R/fslexp.help.R fslr/R/fslbinv.R fslr/R/toffset.R fslr/R/pixdim.R fslr/R/fslrecip.help.R fslr/R/flirt_apply.R fslr/R/fslfill.help.R fslr/R/fslnanm.help.R fslr/R/fsllog.help.R fslr/R/fslasin.R fslr/R/fslroi.R fslr/R/fast.R fslr/R/dtifit.R fslr/R/fsladd.help.R fslr/R/intent_p2.R fslr/R/fslabs.help.R fslr/R/cal_max.R fslr/R/download_fsl.R fslr/R/qform_code.R fslr/R/descrip.R fslr/R/fsldilate.R fslr/R/fslnan.help.R
fslr/vignettes
fslr/vignettes/dti_data.Rmd
fslr/vignettes/fslr.Rmd
fslr/MD5
fslr/build
fslr/build/vignette.rds
fslr/DESCRIPTION
fslr/man
fslr/man/fslstats.help.Rd fslr/man/get.imgext.Rd fslr/man/vox_offset-methods.Rd fslr/man/fsl_anat.Rd fslr/man/melodic.Rd fslr/man/fslbet.Rd fslr/man/fslrandn.help.Rd fslr/man/dtifit.Rd fslr/man/melodic.help.Rd fslr/man/fslrem.Rd fslr/man/fslrecip.help.Rd fslr/man/fslerode.Rd fslr/man/intent_code-methods.Rd fslr/man/fsl_data_dir.Rd fslr/man/fslfill.help.Rd fslr/man/fslroi.Rd fslr/man/fslatan.Rd fslr/man/cal_min-methods.Rd fslr/man/fsl_applywarp.help.Rd fslr/man/fslreorient2std.help.Rd fslr/man/aux_file-methods.Rd fslr/man/have.fsl.Rd fslr/man/sform_code-methods.Rd fslr/man/fslsin.Rd fslr/man/fslsd.Rd fslr/man/fslbet.help.Rd fslr/man/fslorient.help.Rd fslr/man/fslcpgeom.help.Rd fslr/man/fslbin.help.Rd fslr/man/get.fsl.Rd fslr/man/fslindex.help.Rd fslr/man/fsldilate.Rd fslr/man/dim_-methods.Rd fslr/man/download_fsl.Rd fslr/man/fslmaths.Rd fslr/man/susan.Rd fslr/man/fsladd.Rd fslr/man/fslcos.Rd fslr/man/fslrecip.Rd fslr/man/fsl_anat.help.Rd fslr/man/fslasin.help.Rd fslr/man/fslacos.help.Rd fslr/man/fslerode.help.Rd fslr/man/run_first_all.help.Rd fslr/man/fslsub2.help.Rd fslr/man/fsllog.Rd fslr/man/fslsmooth.help.Rd fslr/man/fslrand.help.Rd fslr/man/fslhd.help.Rd fslr/man/eddy_correct.Rd fslr/man/fslabs.Rd fslr/man/fslsplit.Rd fslr/man/mni_img.Rd fslr/man/fslnanm.Rd fslr/man/fslsmooth.Rd fslr/man/fslsplit.help.Rd fslr/man/fslmask.Rd fslr/man/fslcos.help.Rd fslr/man/fslexp.help.Rd fslr/man/run_first_all.Rd fslr/man/fslsqrt.help.Rd fslr/man/fslsin.help.Rd fslr/man/fslbinv.help.Rd fslr/man/descrip-methods.Rd fslr/man/getForms.Rd fslr/man/flirt_apply.Rd fslr/man/fslbin.Rd fslr/man/fslsub2.Rd fslr/man/fslorienter.Rd fslr/man/fslexp.Rd fslr/man/sizeof_hdr-methods.Rd fslr/man/fsllog.help.Rd fslr/man/mcflirt.help.Rd fslr/man/fsladd.help.Rd fslr/man/fslatan.help.Rd fslr/man/mni_fname.Rd fslr/man/flirt.Rd fslr/man/fslsum.Rd fslr/man/datatype-methods.Rd fslr/man/scl_slope-methods.Rd fslr/man/qform_code-methods.Rd fslr/man/fslstats.Rd fslr/man/fslhelp.Rd fslr/man/slice_code-methods.Rd fslr/man/fslbinv.Rd fslr/man/fslswapdim.help.Rd fslr/man/slice_end-methods.Rd fslr/man/fslcog.Rd fslr/man/fast.Rd fslr/man/fnirt.help.Rd fslr/man/fsltan.Rd fslr/man/fslrandn.Rd fslr/man/fslview.Rd fslr/man/intent_name-methods.Rd fslr/man/fslrand.Rd fslr/man/fsl_biascorrect.Rd fslr/man/fslhd.parse.Rd fslr/man/fslindex.Rd fslr/man/fslval.help.Rd fslr/man/fsl_version.Rd fslr/man/fslsqr.help.Rd fslr/man/orientation-methods.Rd fslr/man/fslnan.Rd fslr/man/fslrem.help.Rd fslr/man/fslmaths.help.Rd fslr/man/get.fsloutput.Rd fslr/man/fsldiv.help.Rd fslr/man/fslcpgeom.Rd fslr/man/fsl_applywarp.Rd fslr/man/fslabs.help.Rd fslr/man/fsldiv.Rd fslr/man/fslmerge.Rd fslr/man/data_type-methods.Rd fslr/man/checkout.Rd fslr/man/fslthresh.help.Rd fslr/man/fast.help.Rd fslr/man/fslvolume.Rd fslr/man/fsl_slicetimer.Rd fslr/man/fnirt.Rd fslr/man/magic-methods.Rd fslr/man/fslacos.Rd fslr/man/fnirt_with_affine.Rd fslr/man/cal_max-methods.Rd fslr/man/fslhd.Rd fslr/man/fslview.help.Rd fslr/man/fsl_std_dir.Rd fslr/man/fslfill.Rd fslr/man/fslcmd.Rd fslr/man/fslnanm.help.Rd fslr/man/fslnan.help.Rd fslr/man/fslsqr.Rd fslr/man/flirt.help.Rd fslr/man/fslmerge.help.Rd fslr/man/fsltan.help.Rd fslr/man/fslentropy.Rd fslr/man/fslfill2.Rd fslr/man/fslmul.help.Rd fslr/man/fnirt_with_affine_apply.Rd fslr/man/fslval.Rd fslr/man/fslsqrt.Rd fslr/man/probtrackx.Rd fslr/man/fsledge.help.Rd fslr/man/fslmul.Rd fslr/man/fslorient_wrap.Rd fslr/man/fsldir.Rd fslr/man/fslsub.Rd fslr/man/fslchfiletype.Rd fslr/man/fslsub.help.Rd fslr/man/fslmask.help.Rd fslr/man/slice_duration-methods.Rd fslr/man/fsledge.Rd fslr/man/bitpix-methods.Rd fslr/man/intent_p2-methods.Rd fslr/man/scl_inter-methods.Rd fslr/man/fsl_atlas_dir.Rd fslr/man/fslchfiletype.help.Rd fslr/man/toffset-methods.Rd fslr/man/pixdim-methods.Rd fslr/man/fslreorient2std.Rd fslr/man/intent_p3-methods.Rd fslr/man/fslswapdim.Rd fslr/man/xfibres.Rd fslr/man/susan.help.Rd fslr/man/check_file.Rd fslr/man/fslmean.Rd fslr/man/fslvol.Rd fslr/man/fslasin.Rd fslr/man/intent_p1-methods.Rd fslr/man/fslorient.Rd fslr/man/fslthresh.Rd fslr/man/mcflirt.Rd fslr/man/slice_start-methods.Rd fslr/man/fslrange.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.